Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate GFF295 PS417_01505 gamma-aminobutyrate transporter
Query= TCDB::Q2VQZ4 (536 letters) >FitnessBrowser__WCS417:GFF295 Length = 463 Score = 233 bits (594), Expect = 1e-65 Identities = 144/392 (36%), Positives = 204/392 (52%), Gaps = 10/392 (2%) Query: 33 LKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLALAEM 92 L+Q LK RH+ M++I G IGAGLFVGSG A+ GPA LL Y G +++ LAEM Sbjct: 10 LEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLL-AYAAAGTLVVLVMRMLAEM 68 Query: 93 AVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDINMAV 152 AV P G+F TY R + GF +GW Y W+ V+P E AA+ + W DI + V Sbjct: 69 AVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAWFPDIAIWV 128 Query: 153 WVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGYIGVKY 212 + V ++L +F V+ YGE EF ++IK+ A VGF+ILG+ G + GV + Sbjct: 129 FTLVITLLLTATNLFSVKNYGEFEFWFALIKVVAIVGFVILGLAAIFGFLPTSQVSGVSH 188 Query: 213 WRDPGAF--TSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWRIAIF 270 D F A + FSF GTE+V +AAAES NP + I A+ V WRI +F Sbjct: 189 LFDTQGFMPNGMGAVLAAILTTMFSFMGTEIVTIAAAESKNPGQQITKATNSVIWRIGLF 248 Query: 271 YILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAVLSVA 330 Y+L++FIV ++P NDP L T ++ GI I++ V+ VAV S Sbjct: 249 YLLSIFIVVSLVPWNDPTLAAVGSYQT-------VLERMGIPNAKLIVDLVVLVAVTSCL 301 Query: 331 NSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQGMEIFG 390 NS + ++R + ++ R AP K + G P + V+L LA +F Sbjct: 302 NSALYTASRMLFSLGRRGDAPAVAKRTNKSGTPYWAVLLSTGAAFLAVFANYVAPAAVFE 361 Query: 391 WLLALTGLGFLFVWGSICLAHIRMRAGMKAQG 422 +LLA +G L V+ I ++ +RMR A G Sbjct: 362 FLLASSGAIALLVYLVIAVSQLRMRQKRTAAG 393 Lambda K H 0.327 0.142 0.442 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 578 Number of extensions: 30 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 536 Length of database: 463 Length adjustment: 34 Effective length of query: 502 Effective length of database: 429 Effective search space: 215358 Effective search space used: 215358 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory